You've got the right method there. Most of the time I use Auto-Crossfades because it saves me creating the crossfades!
Another tip you could use is to 'slip' the audio within the part using Ctrl-Alt-Click, and this can be used to make the crossfade work better. A very very small slip can fix an out of phase obvious crossfade without harming the timing (particularly useful with bass).
But I'd have thought that if you were to record 5 takes and pick the bits which are best in time from each one then you'd get a perfect take very quickly...
Also you can always replace out of time bits or dodgy bits with bits from other parts of the performance. This type of replacement is a staple when tidying up live performances because you don't need to get the musician back!
Finally, you'll be surprised what can be hidden in a mix. For example, if you're struggling with a cross fade but it's on the beat of a snare it's quite unlikely you'll hear it in the final mix. Or take that a stage further and actually use another instrument to cover up the problem area! Been there, done that...
Oh, finally again, yes, even though I have the latest Cubase version and I work with excellent musicians, I spend hours tidying up takes towards perfection, and it pays dividends. Sometimes people ask me to listen to their CDs before release and my usual comment is that it's not bad but it needs tidying up, vocals and solos tuning, pops removed, timing tightened, bum notes fixed, etc. So for me, it's a way of life that I picked up working with a top mixing person - to tidy things to a great degree, I think it's worth it. Also your average listener doesn't always know why a song sounds better or worse but chances are if it's off tune or out of time then they'll know that it's not so good. Things just come into focus when you address all the details.